public ViewLibraryPepInfo AssociateMatchingPeptide(ViewLibraryPepInfo pepInfo, int charge, SrmSettingsDiff settingsDiff)
{
var key = pepInfo.Key;
var settings = _chargeSettingsMap[charge];
// Change current document settings to match the current library and change the charge filter to
// match the current peptide.
if (settings == null)
{
settings = _document.Settings;
var rankId = settings.PeptideSettings.Libraries.RankId;
if (rankId != null && !_selectedSpec.PeptideRankIds.Contains(rankId))
{
settings = settings.ChangePeptideLibraries(lib => lib.ChangeRankId(null));
}
settings = settings.ChangePeptideLibraries(
lib => lib.ChangeLibraries(new[] { _selectedSpec }, new[] { _selectedLibrary })
.ChangePick(PeptidePick.library))
.ChangeTransitionFilter(
filter => filter.ChangePrecursorCharges(new[] { charge }).ChangeAutoSelect(true))
.ChangeMeasuredResults(null);
_chargeSettingsMap[charge] = settings;
}
var nodePep = _matcher.GetModifiedNode(key, pepInfo.GetAASequence(_lookupPool), settings, settingsDiff);
if (nodePep != null)
{
pepInfo.PeptideNode = nodePep;
}
return(pepInfo);
}
public PeptideDocNode MatchSinglePeptide(ViewLibraryPepInfo pepInfo)
{
_chargeSettingsMap = new SrmSettings[128];
var nodePep = AssociateMatchingPeptide(pepInfo, pepInfo.Key.Charge).PeptideNode;
if (nodePep == null)
{
return(null);
}
IList <ProteinInfo> matchedProteins = null;
// This is only set if the user has checked the associate peptide box.
var sequence = nodePep.Peptide.Sequence;
if (_backgroundProteome != null)
{
using (var proteomeDb = _backgroundProteome.OpenProteomeDb())
{
var digestion = _backgroundProteome.GetDigestion(proteomeDb, Settings.PeptideSettings);
if (digestion != null)
{
matchedProteins = digestion.GetProteinsWithSequence(sequence).Select(protein => new ProteinInfo(protein)).ToArray();
}
}
}
PeptideMatches = new Dictionary <PeptideSequenceModKey, PeptideMatch>
{
{ nodePep.SequenceKey, new PeptideMatch(nodePep, matchedProteins,
MatchesFilter(sequence, pepInfo.Key.Charge)) }
};
return(nodePep);
}
public ViewLibraryPepInfo AssociateMatchingPeptide(ViewLibraryPepInfo pepInfo, Adduct charge, SrmSettingsDiff settingsDiff)
{
var key = pepInfo.Key;
if (key.IsPrecursorKey)
{
return(pepInfo);
}
var settings = _chargeSettingsMap[charge];
// Change current document settings to match the current library and change the charge filter to
// match the current peptide.
if (settings == null)
{
settings = _document.Settings;
var rankId = settings.PeptideSettings.Libraries.RankId;
if (rankId != null && !_selectedSpec.PeptideRankIds.Contains(rankId))
{
settings = settings.ChangePeptideLibraries(lib => lib.ChangeRankId(null));
}
var isProteomic = pepInfo.Target.IsProteomic;
settings = settings.ChangePeptideLibraries(
lib => lib.ChangeLibraries(new[] { _selectedSpec }, new[] { _selectedLibrary })
.ChangePick(PeptidePick.library))
.ChangeTransitionFilter(
filter => (isProteomic ?
filter.ChangePeptidePrecursorCharges(new[] { charge }) :
filter.ChangeSmallMoleculePrecursorAdducts(new[] { charge }))
.ChangeAutoSelect(true))
.ChangeMeasuredResults(null);
var staticMods = settings.PeptideSettings.Modifications.StaticModifications.ToList();
foreach (var crosslinkMod in Properties.Settings.Default.StaticModList.Where(mod =>
null != mod.CrosslinkerSettings))
{
if (!staticMods.Any(mod => mod.Name == crosslinkMod.Name))
{
staticMods.Add(crosslinkMod);
}
}
settings = settings.ChangePeptideSettings(
settings.PeptideSettings.ChangeModifications(
settings.PeptideSettings.Modifications.ChangeStaticModifications(staticMods)));
_chargeSettingsMap[charge] = settings;
}
var nodePep = _matcher.GetModifiedNode(key, settings, settingsDiff);
if (nodePep != null)
{
pepInfo = pepInfo.ChangePeptideNode(nodePep);
}
return(pepInfo);
}
public ViewLibraryPepMatching(SrmDocument document,
Library library,
LibrarySpec spec,
byte[] lookupPool,
LibKeyModificationMatcher matcher,
ViewLibraryPepInfo[] peptides)
{
_document = document;
_selectedLibrary = library;
_selectedSpec = spec;
_lookupPool = lookupPool;
_matcher = matcher;
_libraryPepInfos = peptides;
_chargeSettingsMap = new SrmSettings[128];
}
public ViewLibraryPepInfo AssociateMatchingPeptide(ViewLibraryPepInfo pepInfo, Adduct charge, SrmSettingsDiff settingsDiff)
{
var key = pepInfo.Key;
if (key.IsPrecursorKey)
{
return(pepInfo);
}
var settings = _chargeSettingsMap[charge];
// Change current document settings to match the current library and change the charge filter to
// match the current peptide.
if (settings == null)
{
settings = _document.Settings;
var rankId = settings.PeptideSettings.Libraries.RankId;
if (rankId != null && !_selectedSpec.PeptideRankIds.Contains(rankId))
{
settings = settings.ChangePeptideLibraries(lib => lib.ChangeRankId(null));
}
var isProteomic = pepInfo.Target.IsProteomic;
settings = settings.ChangePeptideLibraries(
lib => lib.ChangeLibraries(new[] { _selectedSpec }, new[] { _selectedLibrary })
.ChangePick(PeptidePick.library))
.ChangeTransitionFilter(
filter => (isProteomic ?
filter.ChangePeptidePrecursorCharges(new[] { charge }) :
filter.ChangeSmallMoleculePrecursorAdducts(new[] { charge }))
.ChangeAutoSelect(true))
.ChangeMeasuredResults(null);
_chargeSettingsMap[charge] = settings;
}
var nodePep = _matcher.GetModifiedNode(key, settings, settingsDiff);
if (nodePep != null)
{
pepInfo = pepInfo.ChangePeptideNode(nodePep);
}
return(pepInfo);
}
public static int Compare(ViewLibraryPepInfo p1, ViewLibraryPepInfo p2, IList <byte> lookupPool)
{
// If they point to the same look-up index, then they are equal.
if (p1.IndexLookup == p2.IndexLookup)
{
return(0);
}
int lenP1 = p1.SequenceLength;
int lenP2 = p2.SequenceLength;
// If sequences are equal length compare charge and mod count also
int lenCompare = lenP1 == lenP2 ? p1.LengthLookup : Math.Min(lenP1, lenP2);
// Compare bytes in the lookup pool
for (int i = 0; i < lenCompare; i++)
{
byte b1 = lookupPool[p1.IndexLookup + i];
byte b2 = lookupPool[p2.IndexLookup + i];
// If unequal bytes are found, compare the bytes
if (b1 != b2)
{
return(b1 - b2);
}
}
// If sequence length is not equal, the shorter should be first.
if (lenP1 != lenP2)
{
return(lenP1 - lenP2);
}
// p1 and p2 have the same unmodified sequence, same number
// of charges, and same number of modifications. Just
// compare their display strings directly in this case.
return(Comparer.Default.Compare(p1.DisplayString, p2.DisplayString));
}
public static int Compare(ViewLibraryPepInfo p1, ViewLibraryPepInfo p2, IList<byte> lookupPool)
{
// If they point to the same look-up index, then they are equal.
if (p1.IndexLookup == p2.IndexLookup)
return 0;
int lenP1 = p1.SequenceLength;
int lenP2 = p2.SequenceLength;
// If sequences are equal length compare charge and mod count also
int lenCompare = lenP1 == lenP2 ? p1.LengthLookup : Math.Min(lenP1, lenP2);
// Compare bytes in the lookup pool
for (int i = 0; i < lenCompare; i++)
{
byte b1 = lookupPool[p1.IndexLookup + i];
byte b2 = lookupPool[p2.IndexLookup + i];
// If unequal bytes are found, compare the bytes
if (b1 != b2)
return b1 - b2;
}
// If sequence length is not equal, the shorter should be first.
if (lenP1 != lenP2)
return lenP1 - lenP2;
// p1 and p2 have the same unmodified sequence, same number
// of charges, and same number of modifications. Just
// compare their display strings directly in this case.
return Comparer.Default.Compare(p1.DisplayString, p2.DisplayString);
}
public ViewLibraryPepInfo AssociateMatchingPeptide(ViewLibraryPepInfo pepInfo, Adduct charge)
{
return(AssociateMatchingPeptide(pepInfo, charge, null));
}
private void TestBasicFunctionality()
{
// Launch the Library Explorer dialog
_viewLibUI = ShowDialog<ViewLibraryDlg>(SkylineWindow.ViewSpectralLibraries);
// Ensure the appropriate default library is selected
ComboBox libComboBox = null;
ListBox pepList = null;
string libSelected = null;
RunUI(() =>
{
libComboBox = (ComboBox)_viewLibUI.Controls.Find("comboLibrary", true)[0];
Assert.IsNotNull(libComboBox);
libSelected = libComboBox.SelectedItem.ToString();
// Find the peptides list control
pepList = (ListBox)_viewLibUI.Controls.Find("listPeptide", true)[0];
Assert.IsNotNull(pepList);
});
Assert.AreEqual(_testLibs[0].Name, libSelected);
// Initially, peptide with index 0 should be selected
WaitForConditionUI(() => pepList.SelectedIndex != -1);
var modDlg = WaitForOpenForm<MultiButtonMsgDlg>();
RunUI(modDlg.Btn1Click);
ViewLibraryPepInfo previousPeptide = new ViewLibraryPepInfo();
int peptideIndex = -1;
RunUI(() =>
{
previousPeptide = (ViewLibraryPepInfo)pepList.SelectedItem;
peptideIndex = pepList.SelectedIndex;
});
Assert.IsNotNull(previousPeptide);
Assert.AreEqual(0, peptideIndex);
// Now try to select a different peptide and check to see if the
// selection changes
const int selectPeptideIndex = 1;
RunUI(() =>
{
pepList.SelectedIndex = selectPeptideIndex;
});
ViewLibraryPepInfo selPeptide = new ViewLibraryPepInfo();
RunUI(() =>
{
selPeptide = (ViewLibraryPepInfo)pepList.SelectedItem;
});
Assert.IsNotNull(selPeptide);
if (Equals(previousPeptide, selPeptide))
Assert.AreNotEqual(previousPeptide, selPeptide);
// Click the "Next" link
RunUI(() =>
{
var nextLink = (IButtonControl)_viewLibUI.Controls.Find("NextLink", true)[0];
Assert.IsNotNull(nextLink);
nextLink.PerformClick();
});
RunUI(() =>
{
previousPeptide = (ViewLibraryPepInfo)pepList.SelectedItem;
});
// Click "Previous" link and ensure the peptide selected changes
RunUI(() =>
{
var previousLink = (IButtonControl) _viewLibUI.Controls.Find("PreviousLink", true)[0];
Assert.IsNotNull(previousLink);
previousLink.PerformClick();
});
RunUI(() =>
{
selPeptide = (ViewLibraryPepInfo)pepList.SelectedItem;
});
Assert.AreNotEqual(previousPeptide, selPeptide);
// Test valid peptide search
TextBox pepTextBox = null;
RunUI(() =>
{
pepTextBox = (TextBox)_viewLibUI.Controls.Find("textPeptide", true)[0];
Assert.IsNotNull(pepTextBox);
pepTextBox.Focus();
pepTextBox.Text = _testLibs[0].UniquePeptide;
});
int pepsCount = 0;
RunUI(() =>
{
selPeptide = (ViewLibraryPepInfo)pepList.SelectedItem;
pepsCount = pepList.Items.Count;
});
Assert.AreEqual(_testLibs[0].UniquePeptide, selPeptide.DisplayString);
Assert.AreEqual(1, pepsCount);
// Test invalid peptide search
RunUI(() =>
{
pepTextBox.Focus();
pepTextBox.Text = INVALID_SEARCH;
});
RunUI(() =>
{
pepsCount = pepList.Items.Count;
});
Assert.AreEqual(0, pepsCount);
// Test clearing invalid peptide search
RunUI(() =>
{
pepTextBox.Focus();
pepTextBox.Text = "";
});
selPeptide = new ViewLibraryPepInfo();
RunUI(() =>
{
selPeptide = (ViewLibraryPepInfo)pepList.SelectedItem;
pepsCount = pepList.Items.Count;
});
Assert.IsNotNull(selPeptide);
Assert.AreNotEqual(0, pepsCount);
// Test selecting a different library
previousPeptide = selPeptide;
RunDlg<MultiButtonMsgDlg>(() => libComboBox.SelectedIndex = 1, dlg => dlg.Btn1Click());
RunUI(() =>
{
libComboBox.SelectedIndex = 1;
});
RunUI(() =>
{
libSelected = libComboBox.SelectedItem.ToString();
});
Assert.AreEqual(libSelected, _testLibs[1].Name);
RunUI(() =>
{
selPeptide = (ViewLibraryPepInfo)pepList.SelectedItem;
});
Assert.IsNotNull(selPeptide);
Assert.AreNotEqual(previousPeptide, selPeptide);
// If the library is not in the document settings, offer to add the library to the settings.
// If the user declines, add the peptides anyways, but strip them so they do not appear to be
// connected to any library.
RunDlg<MultiButtonMsgDlg>(_viewLibUI.AddPeptide, msgDlg => msgDlg.Btn1Click());
Assert.AreEqual(1, SkylineWindow.Document.PeptideCount);
Assert.IsFalse(SkylineWindow.Document.Peptides.Contains(nodePep => nodePep.HasLibInfo));
RunUI(() =>
{
SkylineWindow.SelectAll();
SkylineWindow.EditDelete();
});
// Test adding peptides offers to add library if not already in settings.
// Test add single peptide.
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(1, 1, 1, 3))
{
RunDlg<MultiButtonMsgDlg>(_viewLibUI.AddPeptide, msgDlg => msgDlg.Btn0Click());
}
RunUI(SkylineWindow.EditDelete);
// Test unmatched peptides are correct.
// One unmatched because its precursor m/z is outside the instrument measurement range
AddAllPeptides(1, 4, 3);
// Verify that everything matches, given a wide enough mass range
RunUI(() => SkylineWindow.ModifyDocument("Change m/z range",
doc => doc.ChangeSettings(doc.Settings.ChangeTransitionInstrument(inst =>
inst.ChangeMaxMz(TransitionInstrument.MAX_MEASURABLE_MZ)))));
WaitForConditionUI(() => !_viewLibUI.HasUnmatchedPeptides);
RunUI(() => SkylineWindow.ModifyDocument("Change m/z range",
doc => doc.ChangeSettings(doc.Settings.ChangeTransitionInstrument(inst =>
inst.ChangeMaxMz(1500)))));
WaitForConditionUI(() => _viewLibUI.HasUnmatchedPeptides);
// Test library peptides are merged without duplicates.
TestForDuplicatePeptides();
// Test library peptides only get added to the document once.
var docOriginal = SkylineWindow.Document;
RunDlg<MessageDlg>(_viewLibUI.AddPeptide, msgDlg => msgDlg.OkDialog());
var filterMatchedPeptidesDlg5 = ShowDialog<FilterMatchedPeptidesDlg>(_viewLibUI.AddAllPeptides);
RunDlg<MessageDlg>(filterMatchedPeptidesDlg5.OkDialog, msgDlg => msgDlg.OkDialog());
Assert.AreSame(docOriginal, SkylineWindow.Document);
// Test missing peptides added.
RunUI(() =>
{
var sequenceTree = SkylineWindow.SequenceTree;
var nodePeps = sequenceTree.Nodes[0].Nodes;
sequenceTree.SelectedNode = nodePeps[0];
sequenceTree.KeysOverride = Keys.Control;
for (int i = 2; i < 10; i += 2)
{
sequenceTree.SelectedNode = nodePeps[i];
}
sequenceTree.KeysOverride = Keys.None;
SkylineWindow.EditDelete();
});
AddAllPeptides();
var docAddBack = SkylineWindow.Document;
// Peptides will be added back in a different order
AssertEx.IsDocumentState(docAddBack, null,
docOriginal.PeptideGroupCount, docOriginal.PeptideCount,
docOriginal.PeptideTransitionGroupCount, docOriginal.PeptideTransitionCount);
TestSamePeptides(docOriginal.Peptides);
// Test missing transition groups added correctly.
RunUI(() =>
{
var sequenceTree = SkylineWindow.SequenceTree;
sequenceTree.SelectedNode = sequenceTree.Nodes[0].Nodes[0].Nodes[0];
sequenceTree.KeysOverride = Keys.Control;
for (int x = 0; x < 5; x++)
{
var nodePep = sequenceTree.Nodes[0].Nodes[x];
var nodeGroups = nodePep.Nodes;
for (int i = 0; i < nodeGroups.Count; i += 2)
{
sequenceTree.SelectedNode = nodeGroups[i];
}
}
SkylineWindow.EditDelete();
});
AddAllPeptides();
var docAddBackGroups = SkylineWindow.Document;
// Check all precursor charges present.
foreach (PeptideDocNode nodePep in docOriginal.Peptides)
{
var key = nodePep.Key;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
var charge = nodeGroup.TransitionGroup.PrecursorCharge;
Assert.IsTrue(docAddBackGroups.Peptides.Contains(nodePepDoc => Equals(key, nodePepDoc.Key)
&& nodePepDoc.HasChildCharge(charge)));
}
}
// Check no duplicate TransitionGroups added.
TestForDuplicateTransitionGroups();
// Test peptides get heavy label modifications.
List<StaticMod> heavyMods15N =
new List<StaticMod> { new StaticMod("15N", null, null, null, LabelAtoms.N15, null, null) };
RunUI(() =>
{
SkylineWindow.SelectAll();
SkylineWindow.EditDelete();
var settings = SkylineWindow.Document.Settings.ChangePeptideModifications(mods => new PeptideModifications(mods.StaticModifications,
new[] { new TypedModifications(IsotopeLabelType.heavy, heavyMods15N) }));
SkylineWindow.ModifyDocument("Change heavy modifications", doc => doc.ChangeSettings(settings));
});
AddAllPeptides();
// All peptides should have a heavy label transition group.
// There should be no peptide whose children do not contain a transition group with heavy label type.
Assert.IsFalse(SkylineWindow.Document.Peptides.Contains(nodePep =>
!nodePep.Children.Contains(nodeGroup =>
((TransitionGroupDocNode)nodeGroup).TransitionGroup.LabelType.Equals(IsotopeLabelType.heavy))));
// Test peptide setting changes update the library explorer.
RunUI(() => SkylineWindow.ModifyDocument("Change static modifications",
doc => doc.ChangeSettings(SkylineWindow.Document.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new List<StaticMod>())))));
AddAllPeptides(1, 8, 3);
// Along with Heavy 15N added earlier in the test, adding this modification means that all library peptides
// will match to the document settings.
StaticMod varMetOxidized = new StaticMod("Methionine Oxidized", "M", null, true, "O",
LabelAtoms.None, RelativeRT.Matching, null, null, null);
var metOxidizedSettings = SkylineWindow.Document.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new[] { varMetOxidized }));
RunUI(() =>
{
SkylineWindow.SelectAll();
SkylineWindow.EditDelete();
SkylineWindow.ModifyDocument("Change static mods",
doc => doc.ChangeSettings(metOxidizedSettings));
});
// Switch to ANL_Combined library
RunDlg<MultiButtonMsgDlg>(() => { libComboBox.SelectedIndex = 2; }, msgDlg => msgDlg.BtnCancelClick());
// User prompted to add library since not in current settings.
RunDlg<MultiButtonMsgDlg>(() => _viewLibUI.CheckLibraryInSettings(), msgDlg => msgDlg.Btn0Click());
// Add single peptide to the document.
RunUI(_viewLibUI.AddPeptide);
WaitForProteinMetadataBackgroundLoaderCompletedUI();
var nodePepAdded = SkylineWindow.SequenceTree.Nodes[0].Nodes[0];
// Because document settings match the library, no duplicates should be found.
AddAllPeptides(0);
// Even though there are two matches in the library for the the nodePep we just added
// to the document (one with light modifications and one with heavy), the two spectrum
// both have the same charge. In this case, both spectrum should be ignored when Add All
// is called.
Assert.AreEqual(nodePepAdded, SkylineWindow.SequenceTree.Nodes[0].Nodes[0]);
Assert.AreEqual(3, SkylineWindow.Document.PeptideCount);
// Switch to the Phospho Loss Library
RunDlg<MultiButtonMsgDlg>(() => libComboBox.SelectedIndex = 3, msgDlg => msgDlg.Btn1Click());
// Add modifications to the document matching the settings of the library.
var phosphoLossMod = new StaticMod("Phospho Loss", "S, T", null, true, "HPO3",
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("H3PO4"), });
var phosphoLossSettings =
SkylineWindow.Document.Settings.ChangePeptideModifications(mods => mods.ChangeStaticModifications(new[] { phosphoLossMod }));
RunUI(() =>
SkylineWindow.ModifyDocument("Change static mods", doc => doc.ChangeSettings(phosphoLossSettings)));
RunDlg<MultiButtonMsgDlg>(() => _viewLibUI.CheckLibraryInSettings(), msgDlg => msgDlg.Btn0Click());
// Again, we should be able to match all peptides since the document settings match use the peptides found
// in the library.
RunDlg<MultiButtonMsgDlg>(_viewLibUI.AddAllPeptides, msgDlg =>
{
Assert.AreEqual(0, (int)msgDlg.Tag);
msgDlg.Btn1Click();
});
// Test losses are being displayed in the graph, indicating that the spectrum have been matched correctly.
WaitForConditionUI(() => _viewLibUI.GraphItem.IonLabels.Contains(str => str.Contains("98")));
Assert.IsTrue(_viewLibUI.GraphItem.IonLabels.Contains(str => str.Contains("98")));
// Associate yeast background proteome
var peptideSettingsUI = ShowDialog<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunDlg<BuildBackgroundProteomeDlg>(peptideSettingsUI.ShowBuildBackgroundProteomeDlg,
buildBackgroundProteomeDlg =>
{
buildBackgroundProteomeDlg.BackgroundProteomePath = TestFilesDir.GetTestPath("yeast_mini.protdb");
buildBackgroundProteomeDlg.BackgroundProteomeName = "Yeast";
buildBackgroundProteomeDlg.OkDialog();
});
RunUI(peptideSettingsUI.OkDialog);
WaitForCondition(() =>
{
var peptideSettings = Program.ActiveDocument.Settings.PeptideSettings;
var backgroundProteome = peptideSettings.BackgroundProteome;
return backgroundProteome.HasDigestion(peptideSettings);
});
WaitForDocumentLoaded(); // Give background loader a chance to get the protein metadata too
RunDlg<TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, transitionSettingsUI =>
{
transitionSettingsUI.PrecursorCharges = "1,2,3";
transitionSettingsUI.OkDialog();
});
// Test add all with the yeast background proteome connected.
RunUI(() =>
{
SkylineWindow.SelectAll();
SkylineWindow.EditDelete();
// Switch to yeast library.
libComboBox.SelectedIndex = 4;
_viewLibUI.AssociateMatchingProteins = true;
});
var addLibraryDlg = ShowDialog<MultiButtonMsgDlg>(_viewLibUI.AddAllPeptides);
// Add the library to the document.
var filterMatchedPeptidesDlg = ShowDialog<FilterMatchedPeptidesDlg>(addLibraryDlg.Btn0Click);
RunUI(() => filterMatchedPeptidesDlg.AddUnmatched = false);
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(4, 10, 13, 39))
{
RunDlg<MultiButtonMsgDlg>(filterMatchedPeptidesDlg.OkDialog, messageDlg => messageDlg.Btn1Click());
}
Assert.IsFalse(SkylineWindow.Document.Peptides.Contains(nodePep => !nodePep.HasLibInfo));
// Test adding a single peptide that matches two different proteins using keep all.
RunUI(() =>
{
SkylineWindow.Undo();
_viewLibUI.ChangeSelectedPeptide("ADTGIAVEGATDAAR+");
});
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(2, 2, 2, 6))
{
RunDlg<FilterMatchedPeptidesDlg>(_viewLibUI.AddPeptide,
filterMatchedPeptideDlg => filterMatchedPeptideDlg.OkDialog());
}
// Test adding a second charge state for that peptide.
RunUI(() => _viewLibUI.ChangeSelectedPeptide("ADTGIAVEGATDAAR++"));
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(2, 2, 4, 12))
{
RunDlg<FilterMatchedPeptidesDlg>(_viewLibUI.AddPeptide,
filterMatchedPeptideDlg => filterMatchedPeptideDlg.OkDialog());
}
RunDlg<FilterMatchedPeptidesDlg>(_viewLibUI.AddPeptide,
filterMatchedPeptideDlg => filterMatchedPeptideDlg.OkDialog());
// Test adding a second charge state - No Duplicates.
RunUI(() => SkylineWindow.Undo());
var docPrev = WaitForDocumentLoaded();
RunDlg<FilterMatchedPeptidesDlg>(_viewLibUI.AddPeptide,
filterMatchedPeptideDlg =>
{
filterMatchedPeptideDlg.DuplicateProteinsFilter = BackgroundProteome.DuplicateProteinsFilter.NoDuplicates;
filterMatchedPeptideDlg.OkDialog();
});
Assert.AreEqual(docPrev, WaitForDocumentLoaded());
// Test adding a second charge state - First Only.
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(2, 2, 3, 9))
{
RunDlg<FilterMatchedPeptidesDlg>(_viewLibUI.AddPeptide, filterMatchedPeptideDlg =>
{
filterMatchedPeptideDlg.DuplicateProteinsFilter =
BackgroundProteome.DuplicateProteinsFilter.FirstOccurence;
filterMatchedPeptideDlg.OkDialog();
});
}
RunUI(() =>
{
SkylineWindow.Undo();
SkylineWindow.Undo();
// Add doubly charged state, no protein association.
_viewLibUI.AssociateMatchingProteins = false;
_viewLibUI.AddPeptide();
_viewLibUI.AssociateMatchingProteins = true;
});
// Add doubly charged state with protein assocation.
RunDlg<FilterMatchedPeptidesDlg>(_viewLibUI.AddPeptide,
filterMatchedPeptideDlg => filterMatchedPeptideDlg.OkDialog()); // First only
// Select singly charged state
RunUI(() => _viewLibUI.ChangeSelectedPeptide("ADTGIAVEGATDAAR+"));
// Test adding peptide associated with the background proteome does not affect any matching peptides that are
// in peptide lists.
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(2, 2, 3, 9))
{
RunDlg<FilterMatchedPeptidesDlg>(_viewLibUI.AddPeptide,
filterMatchedPeptideDlg => filterMatchedPeptideDlg.OkDialog()); // First only
}
var peptideGroups = SkylineWindow.Document.PeptideGroups.ToArray();
int index = peptideGroups.IndexOf(nodeGroup => nodeGroup.IsPeptideList);
Assert.IsTrue(peptideGroups[index].Children.Count == 1);
// Test selecting no duplicates prevents any peptide from appearing twice in the document.
RunUI(() => SkylineWindow.Undo());
RunUI(() => SkylineWindow.Undo());
var filterMatchedPeptidesDlg1 = ShowDialog<FilterMatchedPeptidesDlg>(_viewLibUI.AddAllPeptides);
RunUI(() => filterMatchedPeptidesDlg1.DuplicateProteinsFilter = BackgroundProteome.DuplicateProteinsFilter.NoDuplicates);
RunDlg<MultiButtonMsgDlg>(filterMatchedPeptidesDlg1.OkDialog, messageDlg => messageDlg.Btn1Click());
TestForDuplicatePeptides();
// Test selecting first occurence prevents any peptide from appearing twice in the document.
RunUI(() => SkylineWindow.Undo());
var filterMatchedPeptidesDlg2 = ShowDialog<FilterMatchedPeptidesDlg>(_viewLibUI.AddAllPeptides);
RunUI(() => filterMatchedPeptidesDlg2.DuplicateProteinsFilter = BackgroundProteome.DuplicateProteinsFilter.FirstOccurence);
RunDlg<MultiButtonMsgDlg>(filterMatchedPeptidesDlg2.OkDialog, messageDlg => messageDlg.Btn1Click());
TestForDuplicatePeptides();
// Test peptides are added to "Library Peptides" peptide list if this peptide group already exists.
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(1, 2, 3, 9))
{
RunUI(() =>
{
SkylineWindow.Undo();
_viewLibUI.AssociateMatchingProteins = false;
_viewLibUI.AddPeptide();
_viewLibUI.ChangeSelectedPeptide("AAAP");
_viewLibUI.AddPeptide();
});
}
RunUI(() =>
{
SkylineWindow.SelectAll();
SkylineWindow.EditDelete();
});
// Close the Library Explorer dialog
OkDialog(_viewLibUI, _viewLibUI.CancelDialog);
}
public PeptideDocNode MatchSinglePeptide(ViewLibraryPepInfo pepInfo)
{
_chargeSettingsMap = new SrmSettings[128];
var nodePep = AssociateMatchingPeptide(pepInfo, pepInfo.Key.Charge).PeptideNode;
if (nodePep == null)
return null;
IList<ProteinInfo> matchedProteins = null;
// This is only set if the user has checked the associate peptide box.
var sequence = nodePep.Peptide.Sequence;
if (_backgroundProteome != null)
{
using (var proteomeDb = _backgroundProteome.OpenProteomeDb())
{
var digestion = _backgroundProteome.GetDigestion(proteomeDb, Settings.PeptideSettings);
if (digestion != null)
{
matchedProteins = digestion.GetProteinsWithSequence(sequence).Select(protein=>new ProteinInfo(protein)).ToArray();
}
}
}
PeptideMatches = new Dictionary<PeptideSequenceModKey, PeptideMatch>
{{nodePep.SequenceKey, new PeptideMatch(nodePep, matchedProteins,
MatchesFilter(sequence, pepInfo.Key.Charge))}};
return nodePep;
}
public ViewLibraryPepInfo AssociateMatchingPeptide(ViewLibraryPepInfo pepInfo, int charge, SrmSettingsDiff settingsDiff)
{
var key = pepInfo.Key;
var settings = _chargeSettingsMap[charge];
// Change current document settings to match the current library and change the charge filter to
// match the current peptide.
if (settings == null)
{
settings = _document.Settings;
var rankId = settings.PeptideSettings.Libraries.RankId;
if (rankId != null && !_selectedSpec.PeptideRankIds.Contains(rankId))
settings = settings.ChangePeptideLibraries(lib => lib.ChangeRankId(null));
settings = settings.ChangePeptideLibraries(
lib => lib.ChangeLibraries(new[] { _selectedSpec }, new[] { _selectedLibrary })
.ChangePick(PeptidePick.library))
.ChangeTransitionFilter(
filter => filter.ChangePrecursorCharges(new[] { charge }).ChangeAutoSelect(true))
.ChangeMeasuredResults(null);
_chargeSettingsMap[charge] = settings;
}
var nodePep = _matcher.GetModifiedNode(key, pepInfo.GetAASequence(_lookupPool), settings, settingsDiff);
if (nodePep != null)
{
pepInfo.PeptideNode = nodePep;
}
return pepInfo;
}
public ViewLibraryPepInfo AssociateMatchingPeptide(ViewLibraryPepInfo pepInfo, int charge)
{
return AssociateMatchingPeptide(pepInfo, charge, null);
}
